I plan on doing a bit of both. My intent will be to make the the harness look as if the Z came with the RB in 74. I want the cleanest install possiable. I want to use the stock gauges, and when I can't I'll try an modify the A/M gauges to look stock. This is one very good idea. http://forums.hybridz.org/showthread.php?t=119780
But If your not trying to keep the car looking stock I don't see why you would keep the Z's wires.
This thread is very well written, and will get you going pretty quickly. After that it's up to you to decide how far you want to go into the cars wiring.
I've spent hours looking over schematics trying to see which wires to keep, and which to delete. But man there are a heck of a lot of wires to go through. With hundreds, maybe thousands, of choices to consider.
Let's face it, are we really going to let that engine sit for a few months while we try and figure it out. Hell NO, I want to hear that baby roar yesterday!